Contacts of the strand formed by residues 152 - 159 (chain D) in PDB entry 1Y8R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D ASP* 3.6 22.2 + - + +
128D ALA* 3.5 9.3 - - + -
129D VAL* 3.0 25.3 + - - +
151D ILE* 1.3 78.2 - - - +
153D PHE* 1.3 59.2 + - - +
154D PHE* 4.4 5.8 - - + -
168D ASN 4.1 2.7 - - - -
169D LEU* 3.4 35.7 - - + +
172D HIS* 4.3 13.2 - - - -
317D ALA* 3.6 30.0 + - + -
318D LEU* 4.5 13.6 + - + +
320D GLN* 4.3 16.5 + - - +
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Residues in contact with PHE 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 3.7 5.6 - - + -
131D LEU* 4.0 13.9 - - + -
139D ILE* 3.7 26.0 - - + -
142D VAL* 3.7 13.7 - - + -
143D ASP* 3.2 45.5 - - + +
146D CYS* 3.8 28.7 - - + -
151D ILE 3.2 0.6 + - - +
152D LYS* 1.3 75.0 - - - +
154D PHE* 1.3 87.7 + - - +
155D THR* 4.0 14.1 - - + -
166D PHE* 4.0 9.9 - + - -
167D ALA* 3.4 0.2 - - - -
168D ASN* 2.8 41.5 + - + +
169D LEU* 4.5 0.4 - - - +
216D VAL* 3.8 13.0 - - + -
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Residues in contact with PHE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ALA* 4.6 6.3 - - + -
129D VAL 2.9 18.2 + - - +
130D CYS* 3.8 15.0 - - - -
131D LEU 3.0 18.2 + - - -
152D LYS* 4.4 9.0 - - + -
153D PHE* 1.3 88.0 - - - +
155D THR* 1.3 66.4 + - - +
165D THR* 5.4 0.7 - - + -
166D PHE 3.3 7.6 - - - -
167D ALA* 3.4 31.4 - - + -
169D LEU* 3.8 25.1 - - + -
310D LEU* 3.9 14.8 - - + -
313D GLU* 3.9 20.4 - - + -
314D ILE* 3.5 43.3 - - + -
317D ALA* 3.8 11.7 - - + -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D CYS* 4.8 1.1 - - - -
131D LEU* 3.1 26.0 + - - +
139D ILE* 4.2 19.1 - - + +
153D PHE* 4.0 11.2 - - + -
154D PHE* 1.3 78.6 - - - +
156D GLY* 1.3 61.0 + - - +
157D ASP* 4.7 1.0 + - - -
164D TYR* 3.2 18.2 + - + +
165D THR* 3.5 2.1 - - - -
166D PHE* 2.9 63.1 + - + +
216D VAL* 5.1 1.1 - - + -
310D LEU* 4.0 8.5 - - - +
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Residues in contact with GLY 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.4 16.9 - - - +
131D LEU 3.0 4.5 + - - +
132D THR* 3.5 12.1 - - - -
155D THR* 1.3 81.0 + - - +
157D ASP* 1.3 77.2 + - - +
164D TYR* 3.2 21.5 - - - -
310D LEU* 4.3 6.1 - - - +
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Residues in contact with ASP 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.5 9.2 - - - +
132D THR* 3.5 5.8 - - - +
133D CYS* 2.6 32.8 + - - -
134D CYS 4.4 0.9 + - - +
139D ILE* 5.2 1.0 - - - +
155D THR* 4.7 1.6 + - - -
156D GLY* 1.3 82.2 + - - +
158D VAL* 1.3 66.2 + - - +
159D PHE* 3.3 24.5 - - + -
163D GLY* 3.3 1.9 - - - -
164D TYR* 3.0 53.2 + - + +
250D ARG* 3.0 29.7 + - - +
306D VAL* 4.6 0.3 - - - +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 4.5 8.6 - - + +
157D ASP* 1.3 82.6 - - - +
159D PHE* 1.3 73.2 + - - +
160D GLY 3.9 10.5 - - - +
162D HIS 3.3 8.7 - - - +
163D GLY* 3.8 5.4 - - - -
250D ARG* 5.6 0.2 + - - -
256D ASP* 5.1 4.0 - - - +
297D SER 4.1 4.0 - - - +
298D GLU* 4.2 15.2 - - + +
299D MET 4.2 13.7 - - - +
302D VAL* 3.7 35.2 - - + +
303D CYS* 4.3 20.2 - - - -
306D VAL* 3.9 16.6 - - + -
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Residues in contact with PHE 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D ASP* 3.3 36.3 - - + -
158D VAL* 1.3 81.4 - - - +
160D GLY* 1.3 64.8 + - - +
161D TYR 3.2 0.5 + - - -
162D HIS* 2.6 38.3 + - + +
163D GLY* 4.9 3.1 - - - -
164D TYR* 3.6 27.4 - + + -
242D LEU* 5.5 1.6 - - + -
243D LEU* 4.2 16.4 - - + -
246D LEU* 3.4 42.0 - - + -
247D LEU* 6.1 0.7 - - + -
250D ARG* 3.6 16.8 - - - -
256D ASP* 4.8 9.6 - - + -
257D PRO* 5.8 1.8 - - + -
295D CYS* 3.3 25.5 - - - +
296D PHE 5.2 0.2 - - - -
297D SER 3.7 3.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il